I think the theory is that Kazakhstan (for example) don't learn anything if they end up finishing second in a mini-group of them, Moldova and Andorra and getting knocked out. It's not a perfect situation at the moment but I'm not sure pre-qualification is the answer. UEFA will point to the Faroes getting a couple of good results down the years, Andorra winning last night against Hungary (who made the last 16 of the Euros last year), the steady improvement of some of the smaller Balkan nations down the years, how rancid Turkey were as recently as the early 90s but how they developed through playing better opposition...even Wales are ok these days.
Our calendar allows for all the fixtures so it's no biggie. Of course the games themselves against the palpably out of their depth teams are awful to watch, but no-one's forcing you to turn up or tune in.